Polygenic Score (PGS) ID: PGS001535

Predicted Trait
Reported Trait Use of sun/uv protection (Sometimes)
Mapped Trait(s) sun exposure measurement (EFO_0010729)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC20002267
Released in PGS Catalog: Nov. 25, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_BIN_FC20002267
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 309
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,577 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 94,861 cases
  • , 174,716 controls
]
 European UKB — — — white British ancestry Training + validation cohort (train_val)

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM005190 PSS003830|
African Ancestry|
6,273 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Use of sun/uv protection (Sometimes) — AUROC: 0.5906 [0.57555, 0.60565] R²: 0.03109
Incremental AUROC (full-covars): -0.00144
PGS R2 (no covariates): 0.00136
PGS AUROC (no covariates): 0.48531 [0.46984, 0.50078]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005191 PSS003831|
East Asian Ancestry|
1,652 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Use of sun/uv protection (Sometimes) — AUROC: 0.55282 [0.52505, 0.58059] R²: 0.01545
Incremental AUROC (full-covars): 0.00303
PGS R2 (no covariates): 0.00113
PGS AUROC (no covariates): 0.51387 [0.48597, 0.54177]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005192 PSS003832|
European Ancestry|
24,868 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Use of sun/uv protection (Sometimes) — AUROC: 0.59511 [0.58776, 0.60245] R²: 0.03349
Incremental AUROC (full-covars): 0.0029
PGS R2 (no covariates): 0.00751
PGS AUROC (no covariates): 0.54353 [0.53602, 0.55103]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005193 PSS003833|
South Asian Ancestry|
7,396 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Use of sun/uv protection (Sometimes) — AUROC: 0.55494 [0.54118, 0.5687] R²: 0.01063
Incremental AUROC (full-covars): -0.00239
PGS R2 (no covariates): 0.00017
PGS AUROC (no covariates): 0.49173 [0.47787, 0.50558]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005194 PSS003834|
European Ancestry|
67,387 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Use of sun/uv protection (Sometimes) — AUROC: 0.59313 [0.58866, 0.5976] R²: 0.03328
Incremental AUROC (full-covars): 0.00692
PGS R2 (no covariates): 0.00443
PGS AUROC (no covariates): 0.53162 [0.52709, 0.53614]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS003830 — —
[
  • 1,944 cases
  • , 4,329 controls
]
 — African unspecified — UKB —
PSS003831 — —
[
  • 762 cases
  • , 890 controls
]
 — East Asian — UKB —
PSS003832 — —
[
  • 8,425 cases
  • , 16,443 controls
]
 — European non-white British ancestry UKB —
PSS003833 — —
[
  • 2,556 cases
  • , 4,840 controls
]
 — South Asian — UKB —
PSS003834 — —
[
  • 23,767 cases
  • , 43,620 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)